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Flanigan was born Joseph Dunnigan III in Los Angeles, California. He has said that his father left his mother soon after he was born and that his surname was changed to Flanigan after he was adopted by his stepfather, John Flanigan.[1] Flanigan has three brothers and four sisters. When he was six years old, his family moved to a small ranch near Reno, Nevada.[2]

After graduation, he pursued a writing career. He worked on Capitol Hill[7] and then briefly for several New York City publications, including Town & Country and Interview magazine. On the advice of some of his friends, he studied at the Neighborhood Playhouse, was coached by Gerald Gordon,[8] and then moved back to Los Angeles in 1994 to pursue an acting career.

Flanigan had guest roles in numerous television series including Profiler, First Monday, and Sisters, until he got his breakthrough with his role on Stargate Atlantis as Lt. Colonel John Sheppard. He lived in Vancouver, Canada, where the series was filmed during the week, and flew to Los Angeles during the weekends where his wife and children resided.[9] He additionally wrote for the series and created the stories for the Stargate Atlantis second season episode "Epiphany" and the fourth season episode "Outcast".

In September 2007, scifi.com's SciFi Wire service reported that, "Talent agency UTA filed suit on Sept. 24 against Stargate Atlantis star Joe Flanigan in Los Angeles Superior Court, claiming that the actor owes $99,225 in commissions, according to The Hollywood Reporter; Flanigan's manager, John Carrabino, told the trade paper about the lawsuit: 'I had no idea they did this. This is the first time I'm hearing about this.'" UTA filed a similar lawsuit against actor Wesley Snipes who was equally surprised.[10] This suit was settled in December 2008.

He is best friends with Stargate Atlantis co-star Jason Momoa which Momoa has said in many interviews. They often lived together while shooting the show in Vancouver, and they both lived in Malibu separately during season breaks, where they would surf together. He is also good friends with co-star David Hewlett.

He shares his birthday with former Stargate Atlantis co-star Paul McGillion. He currently resides in Malibu, California.